Premise of the study: Characteristics of rare taxa include small population sizes and limited geographical ranges. The genetic consequences of rarity are poorly understood for most taxa. A small geographical range could result in reduced opportunity for isolation by distance or environment, thereby limiting genetic structure and variation, but few studies explore genetic structure at small spatial scales with sufficient resolution to test this hypothesis. Moreover, few comparative genetic studies exist among infrataxa differing in rarity. Here, we compare genetic variation among varieties of Astragalus lentiginosus differing in range size. Additionally, we ask if genetic structure exists in A. l. var. piscinensis, a rare taxon consisting of several thousand individuals that persist on ~8 km2 of alkaline soil. Methods: We compared genetic variation among 11 varieties of A. lentiginosus differing in range size using a genotyping by sequencing (GBS) approach, which generated 11,475 single nucleotide polymorphisms (SNPs). We characterized genetic structure among subpopulations of A. l. var. piscinensis using a second GBS dataset of 7,274 SNPs and explored associations between genetic structure and environmental variation. Key results: We found no association between genetic variation and range size among varieties of A. lentiginosus. Additionally, despite the extremely small range of A. l. var. piscinensis, we report a well-defined genetic structure among subpopulations associated with microhabitat variation in soil composition. Conclusion: Our results suggest that fine scale genetic structure may exist within other rare Astragalus taxa and that rarity does not preclude the maintenance of genetic diversity in this genus. In compliance with data protection regulations, please contact the publication office if you would like to have your personal information removed from the database.